9LKG | pdb_00009lkg

Ornithine decarboxylase from Lacticaseibacillus rhamnosus

PDB DOI: https://doi.org/10.2210/pdb9LKG/pdb

Classification: LYASE
Organism(s): Lacticaseibacillus rhamnosus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-01-16 Released: 2025-12-24
Deposition Author(s): Kim, D.S., Park, J.H., Adiko, N.N., Seo, H.T.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free:
0.301 (Depositor), 0.302 (DCC)
R-Value Work:
0.278 (Depositor), 0.281 (DCC)
R-Value Observed:
0.279 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Insight into the functional and structural relationship of ornithine decarboxylase and its mutants from Lacticaseibacillus rhamnosus.

Adiko, N.N., Seo, H.T., Ki, D.W., Park, J.H., Kim, D.S.

(2025) Bull Korean Chem Soc 46: 730-742

DOI: https://doi.org/10.1002/bkcs.70035

Macromolecule Content

Total Structure Weight: 303.18 kDa
Atom Count: 22,182
Modeled Residue Count: 2,770
Deposited Residue Count: 2,772
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ornithine decarboxylase	A [auth C], B [auth A], C [auth B], D	693	Lacticaseibacillus rhamnosus	Mutation(s): 0 Gene Names: LRHMDP2_881 EC: 4.1.1.17

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A [auth C], B [auth A], C [auth B], D	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.301 (Depositor), 0.302 (DCC)
R-Value Work: 0.278 (Depositor), 0.281 (DCC)
R-Value Observed: 0.279 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.782	α = 86.75
b = 80.607	β = 80.61
c = 121.822	γ = 70.83

Software Package:

Software Name	Purpose
REFMAC	refinement
Coot	model building
SCALA	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-24

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2022R1A6A3A01087301

Revision History (Full details and data files)

Version 1.0: 2025-12-24
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.